PERFILES DE METILACIÓN EN 38 GENES DE LA REGIÓN CRÍTICA DEL SÍNDROME

DE DOWN (DSCR)

Karla Vinasco Pacheco y Felipe García Vallejo

Grupo LABIOMOLDepartamento de Ciencias FisiológicasEscuela de Ciencias BásicasFacultad de SaludUniversidad del Valle

Universidaddel Valle

Universidaddel Valle

Universidaddel Valle

Universidaddel Valle

Universidaddel Valle

Universidaddel Valle

Universidaddel Valle LABORATORIO DE BIOLOGÍALABORATORIO DE BIOLOGÍA

MOLECULAR Y PATOGÉNESISMOLECULAR Y PATOGÉNESISLABORATORIO DE BIOLOGÍALABORATORIO DE BIOLOGÍA

MOLECULAR Y PATOGÉNESISMOLECULAR Y PATOGÉNESIS

Have an estimated size of 46.944.323 bp with [582 genes and putative genes from the finished sequence of HSA21.

The proteins encoded by these genes fall into several functional categories including transcription factors, regulators and modulators (18 genes); proteases and protease inhibitors (6 genes); ubiquitin pathway (4 genes); interferons and immune response (9 genes); kinases (8 genes); RNA processing (5 genes); adhesion molecules (4 genes); channels (7 genes); receptors (5 genes); and energy metabolism (4 genes). Interestingly,

~1% of the HSA21 corresponds to conserved non-genic (CNG) sequences, that is, sequences that are not "functionally" transcribed and do not correspond to protein-coding genes

EL CROMOSOMA 21

EL SÍNROME DE DOWN

LOS CIRCUITOS DE APRENDIZAJE EN EL SD

ESTRUCTURAS CEREBRALES INVOLUCRADAS EN:

Adquisición de información Procesamiento de información Almacenamiento de la información

HIPOTESIS PARA EXPLICAR EL FENOTIPO DOWN

Several reports on partial trisomy 21 targeted a specific region of human chromosome 21 (part of 21q22.1 to 21q22.3 bands) as a key suspect in causing the major phenotypic features of DS.

It is named as ‘Down syndrome critical region (DSCR)’. The human DSCR contains approximately 38 presumed genes .

LA REGIÓN CRÍTICA DEL SÍNDROME DE DOWN

ID Symbol Name Locus Function1827 RCNA1 Regulator of calcineurin 1 21q22.12 Specific DNA binding transcription factor activity

54102 CLIC6 Chloride intracellular channel 6 21q22.12 Voltage-gated chloride channel activity861 RUNX1 Runt-related transcription factor 1 21q22.3 Transcription factor binding

54093 SETD4 SET domain containing 4 21q22.13 Methyltransferase activity873 CBR1 Carbonyl reductase 1 21q22.13 Prostaglandin-E2 9-reductase activity

388822 MEMO1P mediator of cell motility 1 pseudogene 21q22.12 UKF874 CBR3 Carbonyl reductase 3 21q22.2 Carbonyl reductase (NADPH) activity

23515 MORC3 CW-type zinc finger 3 21q22.13 Zinc ion binding8208 CHAF1B Chromatin assembly factor 1, p60 21q22.13 Histone binding

23562 CLDN14 Claudin 14 21q22.3 Structural molecule activity6493 SIM2 Single-minded homolog 2 21q22.13 Signal transducer activity3141 HLCS Holocarboxylase synthetase 21q22.13 Protein homodimerization activity

53820 RIPPLY3 Ripply transcriptional repressor 3 21q22.2 Transcription, DNA-dependent7267 TTC3 Ttetratricopeptide repeat domain 3 21q22.2 Zinc ion binding

418520 PIGP Proteasome assembly chaperone 1 21q22.2 Phosphatidylinositol N-acetylglucosaminyltransferase257203 DSCR9 Down syndrome critical region gene 9 21q22.13 UKF10311 DSCR3 Down syndrome critical region gene 3 21q22.2 UKF1859 DYRK1A Tyrosine-(Y)-phosphorylation kinase 1A 21q22.13 Protein serine/threonine/tyrosine kinase activity

DESCRIPCION DE LOS GENES LOCALIZDOS EN LA DSCR DEL CROMOSOMA 21

ID Symbol Name Locus Function3763 KCNJ6 Potassium inwardly-rectifying channel 6 21q22.1 Inward rectifier potassium channel activity3772 KCNJ15 Potassium inwardly-rectifying channel 15 21q22.2 Inward rectifier potassium channel activity2078 ERG avian erythroblastosis virus E26 oncogene 21q22.3 Signal transducer activity2114 ETS2 v-ets avian erythroblastosis virus E26, 2 21q22.2 DNA binding transcription factor activity8624 PSMG1 Proteasome assembly chaperone 1 21q22.3 Protein binding

54014 BRWD1 Bromodomain and WD repeat domain 21q22.2 Transcription, DNA-dependent

3150HMGN1

High mobility group nucleosome binding domain 1 21q22.2 Nucleosomal DNA binding7485 WRB Tryptophan rich basic protein 21q22.3 UKF

150082 LCA5L Leber congenital amaurosis 5-like 21q22.2 UKF6450 SH3BGR SH3 domain binding glutamic acid-rich protein 21q22.3 SH3 domain binding

114041 C21orf88 Chromosome 21 open reading frame 88 21q22.2 UKF150084 IGSF5 Immunoglobulin superfamily, member 5 21q22.2 PDZ domain binding

5121 PCP4 Purkinje cell protein 4 21q22.2 Calmodulin binding1826 DSCAM Down syndrome cell adhesion molecule 21q22.2 Protein binding

25825 BACE2 Beta-site APP-cleaving enzyme 2 21q22.3 Aspartic-type endopeptidase activity54097 FAM3B Family with sequence similarity 3, member B 21q22.3 Cytokine activity4600 MX2 Myxovirus (influenza virus) resistance 2 (mouse) 21q22.3 GTPase activity4599 MX1 Myxovirus (influenza virus) resistance 1 21q22.3 GTPase activity

DESCRIPCION DE LOS GENES LOCALIZDOS EN LA DSCR DEL CROMOSOMA 21

POSICIÓN DE LOS GENES LOCALIZADOS EN LA DSCR DEL CROMOSOMA 21RF

6,81 MbDSCR

DETERMINAR LAS MODIFICACIONES EPIGENÉTICAS DE

EN LA DSCR TANTO EN FIBROBLASTOS COMO EN

SUBESTRUCTURAS DEL CEREBRO HUMANO NORMAL .

OBJETIVO GENERAL

Calcular el porcentaje de metilación diferencial en fibroblastos normales y trisómicos

Determinar la metilación de islas CpG en estructuras del cerebro normal

Evaluar la modificación histónica en cerebros normales

OBJETIVOS ESPECÍFICOS

DNA methylation NAME21 project

In the NAME21 project, DNA methylation patterns were analyzed for 190 gene promoter regions on chromosome 21 by using bisulfite conversion and subclone sequencing in five human cell types (leukocytes, fibroblasts, human embryo kidney cell line HEK293, hepatocellular liver carcinoma cell line HepG2 and trisomic-21 fibroblasts derived from a Down syndrome patient).

A total of 28626 subclones were sequenced at high accuracy using (long-read) Sanger sequencing resulting in the measurement of the DNA methylation state of 580.427 CpG-sites.

VISOR GRÁFICO DEL GENOME BROWSER DE UCSC DE LA METILACIÓN EN DIFERENTES TIPOS DE

CÉLULAS

http://genome.ucsc.edu/

METILACIÓN DE LOS PRINCIPALES GENES DSCR EN DIFERENTES TIPOS DE CÉLULAS

Symbol Name Molecular Function RUNX1 Runt-related transcription factor 1 Transcription factor binding CHAF1B Chromatin assembly factor 1, p60 Histone binding CLDN14 Claudin 14 Structural molecule activity DSCR9 Down syndrome critical region gene 9 UKF KCNJ6 Potassium inwardly-rectifying channel 6 Inward rectifier potassium channel activity PCP4 Purkinje cell protein 4 Calmodulin binding DSCAM Down syndrome cell adhesion molecule Protein binding MX2 Myxovirus (influenza virus) resistance 2 GTPase activity MX1 Myxovirus (influenza virus) resistance 1 GTPase activity

(A)

(B)

METILACIÓN DIFERENCIAL EN FIBROBLASTOS NORMALES Y TRISÓMICOS

DATA BASES AND TOOLS OF GENOME BROWSER

DSCR of Chromosome 21

34.908.465-41.720.284 Mb

The UCSC Genes track

CpG islands

UCSF Brain DNA Methylation

MeDIP-seq MRE-seq

CpG Non Metilated CpG Metilated

H3K4me3 ChIP-seq

H3 Histone Modification

http://genome.ucsc.edu/

BASIC STATISTICS

MODIFICACIONES DE LA HISTONA H3 EN LA REGIÓN CRÍTICA DEL SÍNDROME DE DOWN

MODIFICACIÓN DE LA HISTONA H3 EN CEREBRO HUMANO NORMAL

Symbol Name Molecular Function

RCNA1 Regulator of calcineurin 1 Specific DNA binding transcription factor CLIC6 Chloride intracellular channel 6 Voltage-gated chloride channel activity RUNX1 Runt-related transcription factor 1 Transcription factor binding CBR1 Carbonyl reductase 1 Prostaglandin-E2 9-reductase activity

DYRK1A Tyrosine kinase 1A Serine/threonine/tyrosine kinase activity

GENES DSCR CON ELEVADA MODIFICACIÓN DE LA HISTONA H3 EN EL CEREBRO NORMAL

METILACIÓN DE PROMOTORES EL CEREBRO NORMAL EN LA REGIÓN CRÍTICA DEL SINDROME DE DOWN

CpG

BRAIN MeDIP Mean